/usr/lib/python2.7/dist-packages/pysam/TabProxies.pxd is in python-pysam 0.7.7-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | cdef extern from "stdlib.h":
void free(void *)
void *malloc(size_t)
void *calloc(size_t,size_t)
void *realloc(void *,size_t)
int c_abs "abs" (int)
int c_abs "abs" (int)
int atoi( char *nptr)
long atol( char *nptr)
double atof( char *nptr)
cdef extern from "Python.h":
ctypedef struct FILE
char *fgets(char *str, int size, FILE *ifile)
int feof(FILE *stream)
size_t strlen(char *s)
size_t getline(char **lineptr, size_t *n, FILE *stream)
char *strstr(char *, char *)
char *strchr(char *string, int c)
int fileno(FILE *stream)
cdef extern from "string.h":
int strcmp(char *s1, char *s2)
int strncmp(char *s1,char *s2,size_t len)
char *strcpy(char *dest,char *src)
char *strncpy(char *dest,char *src, size_t len)
char *strdup(char *)
char *strcat(char *,char *)
size_t strlen(char *s)
int memcmp( void * s1, void *s2, size_t len )
void *memcpy(void *dest, void *src, size_t n)
void *memchr(void *s, int c, size_t n)
cdef extern from "stdint.h":
ctypedef int int64_t
ctypedef int int32_t
ctypedef int uint32_t
ctypedef int uint8_t
ctypedef int uint64_t
cdef class TupleProxy:
cdef:
char * data
char ** fields
int nfields
int index
int nbytes
int offset
cdef bint is_modified
cdef int getMaxFields( self, size_t nbytes )
# cdef char * _getindex( self, int idx )
cdef take( self, char * buffer, size_t nbytes )
cdef present( self, char * buffer, size_t nbytes )
cdef copy( self, char * buffer, size_t nbytes )
cdef update( self, char * buffer, size_t nbytes )
cdef class GTFProxy( TupleProxy) :
cdef:
char * _attributes
cdef bint hasOwnAttributes
cdef int getMaxFields( self, size_t nbytes )
cdef char * getAttributes( self )
cdef class NamedTupleProxy( TupleProxy) :
pass
cdef class BedProxy( NamedTupleProxy) :
cdef:
char * contig
uint32_t start
uint32_t end
int bedfields
cdef int getMaxFields( self, size_t nbytes )
cdef update( self, char * buffer, size_t nbytes )
cdef class VCFProxy( NamedTupleProxy) :
cdef:
char * contig
uint32_t pos
cdef update( self, char * buffer, size_t nbytes )
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